use with spatial data · Issue #370 · rnabioco/clustifyr (original) (raw)

"At ~50um, spots from the visium assay will encompass the expression profiles of multiple cells. For the growing list of systems where scRNA-seq data is available, users may be interested to 'deconvolute' each of the spatial voxels to predict the underlying composition of cell types. In preparing this vignette, we tested a wide variety of decovonlution and integration methods, using a reference scRNA-seq dataset of ~14,000 adult mouse cortical cell taxonomy from the Allen Institute, generated with the SMART-Seq2 protocol. We consistently found superior performance using integration methods (as opposed to deconvolution methods), likely because of substantially different noise models that characterize spatial and single-cell datasets, and integration methods are specifiically designed to be robust to these differences."

Should compare performance of clustifyr vs seuart anchor approach